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/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* CARET is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BrainSet.h"
#include "CommandVolumeSegmentationToCerebralHull.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
#include "vtkPolyData.h"
#include "vtkPolyDataWriter.h"
/**
* constructor.
*/
CommandVolumeSegmentationToCerebralHull::CommandVolumeSegmentationToCerebralHull()
: CommandBase("-volume-segmentation-to-cerebral-hull",
"VOLUME SEGMENTATION TO CEREBRAL HULL VOLUME AND SURFACE")
{
}
/**
* destructor.
*/
CommandVolumeSegmentationToCerebralHull::~CommandVolumeSegmentationToCerebralHull()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeSegmentationToCerebralHull::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Segmentation Volume File Name", FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addFile("Output Cerebral Hull Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Cerebral Hull VTK Surface File Name", FileFilters::getVtkSurfaceFileFilter());
}
/**
* get full help information.
*/
QString
CommandVolumeSegmentationToCerebralHull::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-segmentation-volume-file-name>\n"
+ indent9 + "<output-cerebral-hull-volume-file-name>\n"
+ indent9 + "<output-cerebral-hull-vtk-surface-file-name>\n"
+ indent9 + "\n"
+ indent9 + "Generate cerebral hull volume and VTK surface from a.\n"
+ indent9 + "segmentation volume file.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeSegmentationToCerebralHull::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get parameters
//
const QString segmentationVolumeFileName =
parameters->getNextParameterAsString("Input Segmentation Volume File Name");
const QString hullVolumeFileName =
parameters->getNextParameterAsString("Output Cerebral Hull Volume File Name");
const QString vtkSurfaceFileName =
parameters->getNextParameterAsString("Output Cerebral Hull VTK Surface File Name");
//
// Read segemtation
//
VolumeFile segmentationVolume;
segmentationVolume.readFile(hullVolumeFileName);
//
// Expand around edges with empty slices
//
int expDim[3];
segmentationVolume.getDimensions(expDim);
const int expSlices = 7;
const int resizeCrop[6] = {
-expSlices, expDim[0] + expSlices,
-expSlices, expDim[1] + expSlices,
-expSlices, expDim[2] + expSlices
};
segmentationVolume.resize(resizeCrop);
//
// Generate hull volume and surface
//
BrainSet bs;
VolumeFile* hullVolume = NULL;
vtkPolyData* hullSurface = NULL;
bs.generateCerebralHullVtkFile(&segmentationVolume,
hullVolume,
hullSurface);
//
// Write the hull volume
//
hullVolume->writeFile(hullVolumeFileName);
//
// Write the hull surface
//
vtkPolyDataWriter* writer = vtkPolyDataWriter::New();
writer->SetInput(hullSurface);
writer->SetHeader("Written by Caret");
writer->SetFileName((char*)vtkSurfaceFileName.toAscii().constData());
writer->Write();
writer->Delete();
//
// free memory
//
hullSurface->Delete();
delete hullVolume;
}
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